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Open AccessArticle

How Machine Learning Methods Helped Find Putative Rye Wax Genes Among GBS Data

1
Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Szczecin, ul. Słowackiego 17, 71–434 Szczecin, Poland
2
Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, ul. Akademicka, 20–950 Lublin, Poland
3
Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Niezapominajek 21, 30–239 Kraków, Poland
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2020, 21(20), 7501; https://doi.org/10.3390/ijms21207501
Received: 28 July 2020 / Revised: 23 September 2020 / Accepted: 7 October 2020 / Published: 12 October 2020
(This article belongs to the Special Issue Functional Genomics for Plant Breeding)
The standard approach to genetic mapping was supplemented by machine learning (ML) to establish the location of the rye gene associated with epicuticular wax formation (glaucous phenotype). Over 180 plants of the biparental F2 population were genotyped with the DArTseq (sequencing-based diversity array technology). A maximum likelihood (MLH) algorithm (JoinMap 5.0) and three ML algorithms: logistic regression (LR), random forest and extreme gradient boosted trees (XGBoost), were used to select markers closely linked to the gene encoding wax layer. The allele conditioning the nonglaucous appearance of plants, derived from the cultivar Karlikovaja Zelenostebelnaja, was mapped at the chromosome 2R, which is the first report on this localization. The DNA sequence of DArT-Silico 3585843, closely linked to wax segregation detected by using ML methods, was indicated as one of the candidates controlling the studied trait. The putative gene encodes the ABCG11 transporter. View Full-Text
Keywords: ATP-binding cassette (ABC) transporters; fatty acid desaturase (FAD), genetic map; glaucousness; large-scale sequence-based markers; Secale cereale L. ATP-binding cassette (ABC) transporters; fatty acid desaturase (FAD), genetic map; glaucousness; large-scale sequence-based markers; Secale cereale L.
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Góralska, M.; Bińkowski, J.; Lenarczyk, N.; Bienias, A.; Grądzielewska, A.; Czyczyło-Mysza, I.; Kapłoniak, K.; Stojałowski, S.; Myśków, B. How Machine Learning Methods Helped Find Putative Rye Wax Genes Among GBS Data. Int. J. Mol. Sci. 2020, 21, 7501.

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